Research workbench
Crystal structure of D. rerio TDP2 complexed with single strand DNA product
Analyse Crystal structure of D. rerio TDP2 complexed with single strand DNA product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FPV
- Type
- protein + DNA
- Length
- 512 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2; DNA (5'-D(P*TP*GP*CP*AP*G)-3')
- EC
- 3.1.4.-
- UniProt
- Q5XJA0
- Ligands
- NA, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 250 | 22% helix, 36% strand | Q5XJA0 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 257 | 24% helix, 34% strand | Q5XJA0 |
| C | DNA (5'-D(P*TP*GP*CP*AP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A, C
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.80 | 0.82 | 100 | GOL, MG |
| 2 | 76 | 0.31 | 0.74 | 19 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 701 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 571 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 4FPV · Crystal structure of D. rerio TDP2 complexed with single strand DNA product · the same entry in another collection · chain A against A, TM-score 1.00
- Q5XJA0 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q5XJA0) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5XJA0
- Elsewhere: RCSB PDB 4FPV · PDBe 4FPV · UniProt Q5XJA0
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